New Dawn
by James dark war
Summary: Ponies had taken their steps into space where they found many other race including Humans all of them had gathered to create the Galaxy council and peace was there but now something from the past will return to put an end of all this Twilight and her friends along with two humans and other race plus a long forgotten race must stop this from happening. comments are welcome.
1. Chapter 1

**New dawn**

**Chapter 1**

Equestria and other kingdoms had taken to space travel they found other race like Humans and many more they even made powers like bionic which can be used to make shields, pick up enemies making barricades was well then they made this little tool which is attached to the arm and can be use to send message and hacking in to thing as well as other things it also come with a energy blade which can cut through armor as thick as 6 inch.

Twilight and her friends where travelling to a dig site where a human camp had dug up something ancient "Okay listen up Twilight you are going to a dig site to pick up an artifact which is a Locust" princess Celestia to Twilight.

"Okay I take it just another peaceful thing" She said to princess Celestia.

"That the thing the camp it self isn't contacting us nothing was heard from it so that why we are sending you and two other down there as well" she stopped and saw the door to the room they where in opening.

As a human wearing black armour came in he wasn't wearing any badge his hair was short and dark brown "James Spec Ops here for this mission" he said not even saluting or anything.

"Wait why is a Spec Ops here for they don't operate with in the galaxy rules" Twilight said to him.

Just then Celestia went by his side "Twilight here is here because this is a human colony and even though the humans are the biggest military in the galaxy the Spect Ops is here to see peace is kept between us and the human" she said as the human went way from them as she looked around as well "And also he is here to inspect you I put your name in for becoming a Spec Ops".

As Twilight gasp "But that the hardest thing to get into they never accept any other race than their own" Twilight said to her shock from this.

"Yes but the human wanted to try and make better peace between the other race so I taken the opportunity to put your name down I wish I could gotten the other in but they were only allowing one in the Spec Ops" she said to her.

"I see I need to think on this but fist I get this mission out of the way" Twilight went off to get two of her friends.

...

Twilight got Applejack and Pinkie Pie together as they where at the ships hanger bay with the human Spec Ops "So are you coming with us" Applejack said to him as the door just open.

They saw him attaching his long range sniper rifle to his armor back "No I work better alone as the saying goes Spec Ops work alone unless it important we work together" he said just before he jumped out in mid air.

…

When the ship landed they three rushed off the ship as it then took off "Okay let head to the dig site see what going on" Twilight said to them as they all rushed off.

"So what do you think stop their communication" Applejack said looking around the ground.

"I am guessing it has to be that thing" Pinkie Pie shouted out pointing to a huge towering robot thing with six legs it was more huger and bigger than a ship could be.

"What is that thing" Twilight said looking at the thing.

"Well we ain't going to find it out by standing here" Applejack said as they moved on.

…

They came to a small camp near the dig site just then these three humans came out of nowhere but they look different they looked like they have been changed and mindless as they came charging towards them "What do we do" shouted out Applejack.

"You have to shoot them" a female human shouted out to them all bring up a assault gun and killing one as they all did the same.

when the place was calm they walked up to the human seeing it was a female human wearing a military uniform her hair was a light oak brown "Who are you" Twilight said to her.

"My name is captain Athena I take it your hear for the thing we dig up" she said reloading her weapon.

"Yes and to find out what happen" Applejack said to her.

"Well as far as I know I was at the barracks until our alarms went off then we saw these thing dragging humans and placing them on these metal spikes turning them into them mindless thing and attack us as well as that huge thing it seems to be stopping out communication with the rest of the galaxy" she said looking around the place seeing dead bodies around.

"Tell me did you see a Spec Ops coming through here" Pinkie Pie said to her.

"Um no wait I did but he turned up at the same time as them all turned and they weren't killing him thought" she rubbing her head.

"Um that couldn't be him okay can you show us the way" Twilight said to her.

"Yes sure it just over that little hill" she said just then they all stopped and saw that huge metal thing leaving the planet as they all walked on.

…

when they got to the top they saw what it was it was a beacon or some kind "Wow it an intact Locust beacon" Applejack said.

"Hay found the Spec Ops" Pinkie Pie shouted as they all saw him laying on the ground with blood.

As they all rushed to him they saw he was shot in the chest "Oh no Canterlot defender we need an immediate pick up with the medic" Applejack said over the radio.

Twilight turned to see Pinkie Pie getting closer to the beacon "No Pinkie Pie" Twilight shouted shoving her out of the way just as a beam hits Twilight filling her mind with image of those robot thing fighting a civilization wiping them out until then she blank out.

…

Twilight slowly open her eyes to see Pinkie Pie next to her with tears coming down her "Twilight your okay" Pinkie Pie said hugging her tightly.

"I am fine" Twilight said just then a doctor unicorn came up to her

"Well I see your majesty is awake you are fine but I can't help notice your brain is doing some amount of active" he said to her.

"I am feeling fine doctor" she said "wait what happen to the Spec Ops".

"Oh him he live to see another he still sleeping next to you" He said pointing to the bed next to Twilight.

As Twilight got up and walked out of the medic room she saw Celestia "Twilight how are you".

"I feel fine what happen" Twilight said to her.

"Well after you pushed Pinkie Pie away from the artifact the thing hit a beam to you and knocked you out for a few good hours and they brought you and the Spec Ops here along with the captain Athena but I can't say for the artifact it was damaged and the Arose ambassador Shari would like to speak to you when you had woken up" Celestia said to her.

"Okay I will talk to her first" Twilight said heading to the comm room.

…

Twilight was in front of a hologram same size of a human same body form only thing was they had blue skying and tentacles hair and their skin was much smoother "Ambassador Shari" Twilight said.

"Princess Twilight I am wanting a report of your mission" Shire said in a female voice.

"The mission was a fail" Twilight said sounding unhappy from saying that.

"A fail how come" she said to her.

"We ran into complication" Twilight said still upset from this.

"I see come to the citadel and meet the rest of the council we will discuss of this failing mission" As Shari went off.

Twilight went to find some place quiet to lay down as the ship was heading towards the citadel where the galaxy council sits to hold meeting for peace of the galaxy the citadel had a ring with five long arms which could close together to keeping safe from attacks.


	2. Chapter 2

**Chapter 2**

When the ship had arrived to the citadel Twilight, princess Celestia, Applejack, Pinkie Pie and Captain Athena went to the council to see them as they saw them Zebras, Griffon, Humans, Arose, Horse and the Ponies all were standing there in a line in front of them "So tell us what had happen" Shire said to them.

"Well we were sent to pick up the artifact and to find out why the communication had stopped when we landed we saw this huge metal robot thing much tall that anything we have ever seen" Twilight said to them.

"Mm can you show us what this thing looks like" A human male said to her.

"No I can't I never taken a picture of it anyway when we arrived at the camp we were attack by these mindless humans they seemed different they changed we engage them with captain Athena here who we asked if she saw any Spec Ops pass by there" Twilight said to them taking a break.

"Yes James went there"the human spoken again.

"No sir the Spec I saw was different from James this Spec went towards the enemy and wasn't being shot at" captain Athena spoken out to him as the room filled with gasp as there was crowd watching.

"What we never sent two we only sent one are you implying that one of our best soldiers in the humans army that we have taken and placed him in the rank of Spec Ops has gone rogue" the humans said to her.

"No sir I am not I am only saying that when I saw James on the ground I saw a different Spec ops there" she said to him.

"Any way carry one" Shari said before any one could say anything.

"Well we managed to get to the artifact with out any more trouble that when we saw James on the ground with a gun shot to his chest he is still knocked out we called for a pick up until I saw commander Pinkie Pie getting close to the thing as I shoved her out of the way I was hurt with a beam it placed image of a civilization being wiped out then that was it" Twilight finished off saying to them.

As they all looked puzzled to it "And your aware of this artifact had been destroyed by this" a zebra ambassador said to them as they nodded.

"I still don't believe one of our Spec Ops had gone rogue with this thing or ever what is this thing and I may have your name removed from the Spec Ops that way it will stop you from being one of them" he said to her.

"Not so fast" they all heard a male voice from behind as they gasp seeing it was James up and walking well nearly walking he was limping "I saw who it was it was a Spec Ops Thomas my old friend I have solid proof" he said pulling a disk out and placing it in a disk player as it played.

"Thomas what are you doing here" they heard James said "Oh the council sent me here to help out" they heard the other male voice "But I wasn't aware of this" James said "Last min thing you know" they heard Thomas saying "Yer do you know what happening here" James said to him"No I just arrived here" they then hear a click noise of a gun "Thomas what are you doing" then a bang of a gun being shot "Sorry old friend but my work can't be interfered with sorry I meant mine and Harvester work you will understand" that was the last they heard of it playing.

As they all looked towards the human ambassador "Well I am shocked to hear this one of our most trusted and loyal soldier has gone rogue mad we will stop his payment and take him off the Spec Ops list stripping his rank and seizing all his resources" the human said pushing a few thing on the tool on his arm.

"What about this Harvester thing he said" Applejack shouted to them.

"As far as we know this Harvester was once a robot race but some how disappeared it myths thought but we have to stop Thomas from doing what ever he is planning on first" a female ambassador of the horse said.

"Then why don't you send your fleet to get him" Applejack shouted out to them.

"And cause a war in the galaxy we will not be held responsible for starting a war on a planet" said the female horse ambassador said to Applejack.

"But a small team could move around undetected!" the zebra ambassador said placing a hoof to her chin.

"Yes but who" said Shire to them all.

"Send me I can get him with my friends" Twilight shouted out to them all.

As they all looked to each other some were nodding other were unsure "ambassador Ryan I think we have all come to agreement" Shire said to the human ambassador.

As he sigh "Yes I agree princess Twilight please step forward" the Ryan said as Twilight looked around seeing lot more other coming around to watch what happing as she did "Twilight a Spec Ops is the back bone of the galaxy council they are the right hand of the council" Ryan said then faced Shire.

"They deal with mission in their way they see fit that either through violence or peaceful the mission always comes first to their eyes they only answer to the council them self" Shire said then facing the horse ambassador.

"Spec Ops aren't picked but rather forge from the fires of courage and brave beyond anything called for they are the first and the last line of defence to the galaxy" he said to Twilight the facing back to Ryan.

"Spec Ops gets the best of training, weapons and anything else they need to get the mission done by order of the Galaxy Council and on behalf of the humans army I welcome the first non human into the Spec Ops you have done your kind proud" he said pushing a few buttons as the crowed all cheered out.

"Its an horner" Twilight said facing her friends.

"Well Twilight you will need a ship and a crew from now on I am stepping down as the captain of Canterlot Defender the ship and crew are now under your command treat her well" Celestia said to Twilight.

"Thank you princess Celestia what about you" she said to her.

"I am staying here on the Citadel to do my part for our kind from keeping the peace just remember Twilight you were a Pony first before becoming a Spec Ops now if you all excuses me I will need to get going to my office" Celestia said leaving them all alone.

Just then Shari came up to them "princess Twilight we have some lead to Thomas your mission is to bring him in any way you want now we believe that one of our own Arose shaman is working with Thomas she is close friend to him her name is Matriarch Sharon and she has a daughter but we don't know is the daughter is working with them as well she is an expert on Locust empire the one that vanished with out a trace and left those FTL space ports and the Citadel even our ships reactor core are made from their techs her name is Rusher her location is at a dig sight in Horizon in the Travers Cluster" she said to Twilight.

"Any thing else" Twilight asked her.

"Yes he has a lab on Frozen Snow we will send a small team there to scout it out for you" She said to her then leaving them all.

"Um commander Twilight may I come along with you for the pay back for hitting my home" Captain Athena said to her.

"Welcome aboard then" Twilight said as they both saluted to each other.

"Well just wait till the rest of the Spec Ops hears this welcome to the rank" he said shacking her hoof "And I like to come with you and on the mission were you get Thomas but I want to be the one that shoot him for shooting me in the chest" he said to her.

"Sure thing" she said to him as they all moved out to the ship.

…

When they got onto the ship Twilight was approached by a stallion earth pony "Commander we had just received the location for the two mission and we have placed it in the nav point and also can I suggest you don't allow the two human to have accesses to our files such as the ship like the weapons, shields and other things" he said to her.

"I know your worried but we need allies to fight a war as well I can't just lock them up in the laundrette room for the rest of the travel and where are they both anyway and why are you so concern" Twilight said to him.

"It just that Spect Ops he brought a laptop on board and they both are in the War Command Room" he said to her as Twilight as she walked off calmly.

…

When she arrived she saw them both talking away and saw the laptop it looked different though like it was more advance than any other laptop she has seen "What is that.

"Ah this is a Spec Ops laptop you will get one it deals with your missions setting them from most important to the least important and sort out your message and also gives your advice on weapons to use on the missions it also does other thing like hacking, description of codes and cyber warfare it one of the most important equipment we have as Spec ops it very light and small so it easy to carry around" he said showing it off just then a small blue female human came up on the laptop.

"Hello" it said in a female voice.

"What that an AI" said Athena.

"Correct Captain Athena" she said to her.

"Wow how did she new my name" Athena said stunned from this.

"I am the AI for James I help him out in battles and advice him in battle planning as well inform him of who the target is I can accesses every files from humans to ponies it my job as being an AI for Spec Ops" she said to them all then facing Twilight "Commander Twilight I have received a message about your Laptop it shall be arriving very soon with an AI of your choice" she said.

"Um thank you" Twilight said to her as she went off line.

"So where is we are going" James said.

"We are heading for Horizon first to get the daughter" she said as they all settled in for the journey.


	3. Chapter 3

**Chapter 3**

When Canterlot Defender arrived over a planet with grey and green Twilight was at the hanger bay with Rainbow Dash and Rarity as they climbed on the shuttle to take them down to the spot "Okay we are after an Arose Matriarch daughter her name is Rusher she is an expert on the Locust Empire so keep your eyes open as well no enemy is in sight but just in case" Twilight said to them both as they nodded.

…

When they jumped off the shuttle they saw a door leading into the mountain as Rarity pushed a button and the door opened they saw from the catwalk a huge Locust ruin it had three levels at the bottom they saw a Arose trapped in some kind of blue field "Okay let get down there" Twilight said just then those mindless Humans came back but some of them had guns on them.

As they rushed to elevator killing the mindless Humans as they go Twilight pushed a button to activate the lift to go down.

Half way down they saw one of the mindless human down at the bottom running out of nowhere with a rocket launcher "Hang on" Rainbow Dash shouted as the rocket hits the lift and it came crashing down on top of the mindless human.

"Is everyone okay" Rarity said getting seeing her friends nodding as they all then got up and walked towards the Arose "Hello are you here to help" she said to them.

"Yes I am Twilight what happen" Twilight said to her.

"Thank the goddess I don't really know it some kind of Locust security field I must have done something I shouldn't have please get me out of here you have to find some way to get behind me to use the consul to shut this thing down.

"What about that" Rarity said pointing to a huge round long pipe thing with teeth's.

"Yes the mining drill it should cut through the wall allowing you to get behind me the code is 4893" she said as Twilight pushed the code in and the thing then charged forward into the wall making a hole in the wall.

As they came through they were inside and behind Rusher "Okay that panel there should deactivate this field" she said as Twilight pushed a few thing and the blue field went off as she got up "Thank you for helping me" she said.

Just then the whole building shaken about "What was that" Rainbow Dash said looking around.

"I am guessing the drill must have made this building unstable we must get out of here now" Rusher said to them.

"Pilot we need an immanent pick up" Twilight shouted over the radio.

"Roger that" the pilot said back as they started running to the exit.

While running they meet those mindless humans running about the place with guns trying to get them when they open the door they saw the Canterlot Defender landing down to picked them while a couple of troops came to take care of the enemy.

…

When Twilight and all her friends along with James and Athena and Rusher was sitting in the debriefing room "So your mother is working with Thomas" Applejack said to her.

"Yes it seems that way but before any one of you jump to any idea I am not like my mother" she said to them all.

"Okay we were told you could help us find what Thomas is after" Twilight said to her.

"No why" she looking puzzled.

"We were on a mission to pick up a Locust beacon but we ran into some complication and it was destroyed but before it was it place some image in my mind" Twilight said to her.

"What really if you want I can connect my mind to yours to see" she said standing up with excitement in her voice.

"Sure" Twilight said then standing up as well.

"Clear your mind let you soul leave your body and take hold of the force that binds us all together" Rusher spoken while slowly getting closer and closing her eye just then she open them as they changed from her normal white with blue to a fully black "connect".

As those same image came flashing back to her just as it went away quickly as Rusher pulled back slowly "I am impress a lesser mind would have gone mad with that gift" she said.

"Did you make anything out of it" Twilight said to her.

"No I couldn't it was unclear but I am guessing what we need is another one of those beacons" she said to her then rubbed her head looking like she was going to faint.

"Are you okay" Fluttershy said to her.

"Yes it just that mind connecting it take a lot of energy out of me I think I will go and have a lay down for a few min" she said to her.

"I agree every one is dismissed" Twilight said as everyone got up and walk away.

"Princess Twilight the council is connecting with us" the pilot said to her.

"Okay patch them through" she said just then Shari and Ryan came up on the hologram.

"How did the mission go" Shire said to her.

"It went perfect we got her" Twilight said to them both.

"I hope your taken the right security protocol" Ryan said to her.

"She can't be with them those mindless humans where there trying to kill her they had weapons as well" Twilight said to him.

"And was it necessary to destroy a Locust ruin" Ryan said to her.

"Those thing where surrounding that place and my team nearly died in there" Twilight said to him with a bit of anger in her voice.

"Of course we agree Commander Twilight the mission must come first" Shire said to her calm them both down "we will be waiting to hear from you on your next mission" as they both went off line.

…

When Twilight was in the WCR with James she saw he was looking over CCTV on their missions "What are you doing".

"Oh I am just wondering Serena alerted me that on our mission for the beacon she said that some of our files were transferred on another memory unit but those files were about the research on that beacon and also some of our weapons systems and I went through all the CCTV on that day and look what I found" James said pushing the play button.

As they watch the CCTV showing building just then these three small looking planes not bigger than a human coming down from the sky as those mindless humans came after them as they shot them down just then a human size creator with two legs they couldn't tell what it actually look like it was wearing some sort of wired armour.

Just as Rusher was passing she caught something on the CCTV "What pause it there" she said as they did "Zoom in on that one" she pointed to the creator as they saw it was a badge of a flag with a claw I saw that badge" she said.

"That badge belongs to the Locust Empire" Serena said to them.

"What but aren't they no longer here" Twilight said to her.

"Yes nothing remains of them no weapons and no armour only their dead cities and temples I seen those badge on building looking like some kind of fort like a military base or a government building" she said to them both.

"Well what ever it is they are the ones that hacked into our computer and stolen our files on the beacon well we will never find out the now what our next action" James said just as a stallion pony came up to Twilight.

"Yes" Twilight said to him.

"Princess this came for you" he said giving her a laptop it was the same as James laptop.

"Ah it your Spec Ops laptop" James said cheerfully as Serena came up.

As Twilight open it up and switched it on "Hello I am Lion" a blue hologram of a stallion earth pony.

"Can I talk to it" Twilight asked James.

"Yes you can you see the AI is active once you touch the laptop it can tell what your choice is of an AI so it has the same mind as you and the same like as you" James said then facing Serena "Say hello".

"Hello my name is Serena" she said facing him.

"Hello Serena" he said as they smiled at each other.

"Okay where was I yes we are going to the Frozen Snow next where there should be a company called Exo corporation where they deal with armour and there should be a lab there belongs to Thomas but for now let settle down it be a long travel to there" Twilight said as they all agreed on that.


	4. Chapter 4

**Chapter 4**

Twilight was in the cockpit of the ship as they arrived at the next mission the lab in Frozen Snow as they were nearing a building "Ground control this is Canterlot Defender can we land" the pilot said.

"Canterlot Defender we don't have you scheduled to land here" the dock control was saying to them.

"We have two Spec Ops on board and wish to dock" the pilot said to the dock control.

"Okay your clear to dock at docking bay 4" the dock control said as the pilot smiled and brought the ship in to the dock.

…

Twilight had Fluttershy and Applejack with her as James and Athena and Rusher were coming to "So James why are you coming" Applejack said to them both.

"Oh I am going to scout this building out and plus Athena wants to come with me as well as Serena" he said to them all as they were waiting for the door to open.

"And I am coming because if my mother is here then you need my biotic to help defeat her" Rusher said just as the door opened and they all walked off the ship and down the walkway towards the four armed guards two ponies and two humans.

"Halt that close enough we are sorry but we have to take all your weapons" the human female said out front of the group.

"Really no one takes my weapon" James said to her as Athena and James pulled out their pistols.

"I will give the count to three to give up your weapons" she said as the three guards behind her pulled their out as Twilight and her friends were watching this "1, 2, 3..." she was cut off by some one shouting over the com.

"Captain stand down Spec Ops are allowed to have weapons" the voice was a female.

"Dam it okay on you all go through" she said stepping aside to let them walk on.

Twilight came to the reception where there was four turret guns "Come through they will not attack please excuses the captain she was only doing her job" she said to them all.

"Thank we are here on business" Twilight said to her.

"Yes you will need to see the head of the building MRS Callus he is in his office through those door and on you left down the stairs" she said as they nodded and walked on.

When the door opened they saw they were in a huge lobby as there was lot of race here all of them either scientist or businessmen all working or chatting away as they head down stairs they saw armed guards over the place.

When they came to the door and Applejack chapped on the door "Yes Yes come in" a male voice said in the office as they all walked in and saw an Encore a smooth skin creator with four eyes this was one of many race through out the galaxy "Mm Commander Twilight" he said to her.

"How did you knew me" Twilight said stunned from this.

"My name is Husker head of this building for Exo Corporation my boss has sent word about you the very first non Human into the Spec Ops I am please one of many race had managed to get into it now I have been told to help you out as much as possible but I can't tell you everything we take pride in our customers privatise" he said holding a little data pad.

"I see has anything passed through the front lately" James asked him.

"Um a Matriarch Sharon here on behalf of Thomas she came with a personal escort and a two heavy crates which passed weapons check" he said to them.

"My mother is here" Rusher said sounding surprised that she is here.

"What type of cargo did she came in with" Applejack said to him.

"Like I said two heavy cargo sealed and locked they passed the weapons check so we had nothing to fear" he said to her.

"What about these escorts" Fluttershy asked him.

"Commandos elite we let them through because we have more than enough guards to deal with them" he said to them all.

"Don't underestimate a Arose commando elite they are powerful" Rusher said to him.

Where did she go" Fluttershy said to him.

"They had gone to lab 45 there is a tram that will take you there directly there it is at the far end of this building you can't miss it" he said to them then facing back to the computer.

"Thank you" Twilight said as they all walked out of the office and looking around "What wrong with them" Twilight said as everyone in the room was watching them.

"They are scared of us they know who we are and they are hiding secretes in their little labs that they don't want us to know about okay I and Athena plus Serena are going to some place we will stay in contact with you as they two went off with the small tool in his arm.

…

When they arrived stepping onto the tram "So these commandos are the powerful" Applejack said to Rusher.

"Yes they are they are the best of us and can handle anything that comes in their way" Rushed said as the tram moved out of the station and along the long dark tunnel.

"James where are" Twilight said over the radio.

"We are at the lab 45 but there is a problem you will come across I can't really tell what going on" James said as he went off line.

"Commander Twilight I have recently hacked into the company com it appears that they have a problem down at a lab which they call the hot lab and that they aren't letting any one in or out" the pony AI said to Twilight.

"Um thanks" Twilight said still a bit shy from the AI thing.

…

As the tram stopped and they all walked off seeing human guards all setting up walls and turrets guns "What who are you" the male one in charge said.

"I am a Spec Ops and I am here on an investigation has a Arose came by" Twilight said to him.

"I see well there was one and a bunch of Commandos came by but they were here to help clean up what ever happen down there" he said saluting to her.

"I see what happen down there" Fluttershy said to him.

"Um I am sorry but I don't really know all the info myself but I can give you access to them here take this lift down to it" he said pushing a few buttons as the lift down unlocked.

"Thank you" Fluttershy said as they all walked in the lift as it door closed then started to go down.

"Twilight we have something here that is amazing we are bringing it back on to the ship" Athena said to them.

"What is it" Twilight said over the radio.

"We don't yet but once your done there you should take a look" James said as they went off line again.

…

When the lift reached the bottom and the door open as they saw Matriarch Sharon on a platform above them "I see that guard let you in I should have killed them while I had a chance tell me by bring my own daughter into this you think I would give up easily" she said facing them all.

"She is here on her own terms" Applejack said to her.

"I don't believe your words ever since your kind was found I always saw they were liars tell me did you tell them everything about me" she said facing her daughter.

"What could I say mother the fact that I see you here right now fighting the galaxy what can I say about that do you expect me to tell them how to beat you" she said sound hurtful about this.

"Tell me Commander Twilight have you ever faced an Arose Commando Elite very few has ever survived" she said as her biotic powers turned her blue and few female Arose commandos came out of nowhere.

As they all take cover firing their weapons to the commandos the AI pony popped up "May I suggest you use an EMP grenade that would take down their shield for a few min allowing you to kill them or injure them" Lion said as Twilight nodded and pulling out a blue grenade pulling the pin and fling it as it exploded and a blue field hurt the commandos taking their shield off and Applejack, Twilight and Fluttershy fired at them killing them.

Just then Sharon and Rusher was fighting each other with their biotic fling thing towards each other just as those mindless humans came out of nowhere and along with more Commandos as Applejack pulled an EMP on them as their shield were off and they started to kill the enemy off while the mindless humans were running towards them.

As they where fighting the mindless Twilight saw Rusher using a gun to fire on her mother as they both were now shooting each other.

After they had dealt with the mindless humans Twilight Rusher was finished fighting as well as they walked up to Rusher seeing her next to her mother who was dyeing "Mother" she said to her.

"Daughter I am sorry I was hoping to stop Thomas but his ship Harvester what too mush for it reduced my mind into nothing taking over my body listen you have to stop him goodbye my little child mother shall see you when that sun rise" as she closed her eyes.

"No mother" Rusher said with tears coming from her.

As Twilight felt it was best to leave her some time as she approached a huge long tank as she saw a weird six leg creator in it with three long tentacles "What are you" Twilight said quietly.

Just then a voice called out "I am the queen of Arachnid" the creator said.

"Wait I thought you were all wiped out" Applejack said to the creator.

"We are the lone survivor of the war we were nothing but an egg we were kept because we knew the location of a lost FTL Space Port she needed it location which we gave her and she had send it to some one we can give you the location but we ask can you free us from this torment" the creator said to Twilight looking her eye to eye.

"What no wait her kind fought the galaxy" Rusher said getting up and walking to the tank.

"We don't seek war we have listen to our kind die out from their own mistake we only want to live in peace we want to teach our children of no war where they can live in harmony" the queen said to her.

"Where would you go" Twilight said to her.

"We will go to a planet that is not habitant on it and we will make children's and teach them of peace so that one day our race may come back and be seen as a friendly and not a hated race" she said to her.

"Okay I am letting you go" Twilight pushed a few buttons as the tank door open and the queen said it thanks and left.

"I hope you know what your doing" Rusher said to her as them made their way back as Fluttershy had gotten the location for the FTL Space Port.

…

When they al arrived back on the ship and left the building Twilight and the others all rushed to the WCR where the rest of her friends and Lion, Serena, Rusher and James was looking over this metal thing it looked like a small fighter plane "So this is the thing where did you find it" Applejack said looking over the thing.

"We found hacking into a bunch of computer at the building it seems to be downloading files that involved with the Locust Empire so we though to attack it and bring it back because that is the same thing we saw on the CCTV" James said to them all.

"Me and Lion have placed our theories together and we have something we have pulled up a bunch of pictures of the ruins of the Locust and there are some drawings of that type of plane" Serena was cut off Rainbow Dash.

"Wait are you saying that thing is a Locust Techs" Rainbow Dash said looking at the thing.

"Well it appears to be but we can't hack into the thing it security it well advance more advance than any of us so we can't get any info out of it" Serena said as they sign with disappointment.

"Okay we will keep this thing lock up in the cargo bay the now and that location where is it" Twilight said to Fluttershy.

"It seems to be in the Rough Cluster what could be there" Fluttershy said thinking.

"Koran it is a huge ruin of the Locust Empire the planet is cover with cities belonging to them" Rusher said to them all sounding excited by this.

"Okay every one is dismissed one of you take this thing down to the cargo bay and make sure Pinkie Pie doesn't get in their to play about with this thing.

As every one moved out "Um princess the council would like to hear your report" the pilot said to her.

"Okay patch them through" Twilight said as Ryan and Shari came up on the hologram.

"Commander Twilight am I reading this right you let a queen Arachnid go" Ryan said sounding unpleasant by this news.

"She knew why her kind had to wipe out she was willing to help us and she only wants peace now for her kind" Twilight said to him.

"Yes we have the location Twilight you will need to come back to the citadel to meet the council that be all" She said as they went off.

"Pilot set a course to the citadel" Twilight shouted out.

"Already done we will be there about an hour" the pilot said back as Twilight went off to get some rest.


	5. Chapter 5

**Chapter 5**

When they all arrived back to the Citadel where Twilight was with the galaxy council along with Celestia "Twilight excellent work the council is ready to take more action" Celestia said with a joy in her voice.

"Yes what your princess has said is true our fleet is ready to handle Thomas fleet if they turn up here or any where in the galaxy" the horse ambassador said to her.

"What about the Koran" Twilight said to them.

"Commander Twilight Koran need to be dealt with a more peaceful solution" Ryan said to her.

"But what ever is down there Thomas is after it" Twilight said to him.

"Twilight please see this from our point of view Koran is an important part of history to the Locust Empire" Shari said to her calming the place down.

"Then send me I can go after him" Twilight said to them all.

"Twilight this is becoming very misbehave of you think of what you have already accomplish now I suggest you return to your ship but the ship is grounded" the zebra ambassador said to her.

"But you can't be" she was silence by Celestia.

"Twilight please do what they have said I will see you later" she said as Twilight went off in an angry mood.

…

Twilight was on the ship alone thinking about what just happen then James came up to her "Hay what wrong" he said.

"The council won't listen to me" Twilight said sounding upset.

"Then what are you going to do" James said to her.

"What can I do they have ground the ship I can't ask the dock control to let us go" Twilight said to him angry.

"Look I can see I was once in this situation I thought hard then I said to myself you know what to hell to what the council ordered I broke against them four times in my carer and look I am still here so sometime you have to brake a few rules now and then" James said cheering her up.

Just then Athena came rushing in "You two come quick to the cargo bay that thing is coming around" she shouted running down to the cargo.

…

When they arrived they saw every one was there even Serena and Lion was there as they saw that little fighter plane was coming around as they saw two red dots blinking on "What will happen" Pinkie Pie said looking at the thing.

"Where am I" the thing said in a robotic sound.

"What" They all shouted out.

"Where am I" the thing said to them all again.

"Um your on a ship called Canterlot Defender" Twilight said to it "Can we ask you what are you".

"I am the 100 Self Aware Fighter Air Plane or SAFAP for short" the plane said to them.

"What your name" Applejack said to it.

"I am SAFAP the others are the same we are all the same name SAFAP" it said to her.

"Okay where did you come from" Athena said to it.

"I can show you" it said to them.

"I wish you could but we are grounded" Twilight said sounding sad from that.

"Princess Twilight Princess Celestia want to meet you at the All Night club" the pilot said over the radio.

"Got it" Twilight said leaving the group.

…

"When Twilight arrived she saw Celestia with Shari sitting down at a table "Princess Celestia I want to ask and I am sorry for saying this but why couldn't you help me out you believe me" she said sounding frustrated.

"Twilight I do but I can't just go against the council as well it was all done through votes I tried to warn you before you dock but I couldn't" Celestia said sound sorry for her.

"What about you councillor Shari" Twilight said facing her.

"Twilight I am always on any one side I am a neutral but however I too believe you but the council had out voted me to allow you go but I have come up with a plan" she said to her smiling.

"What the plan" Twilight said sounding curios to it.

"It simple the one who has control over the docks is the Zebra ambassador he was the one who had authorised the lock down but I can sneak into his office and hack into his computer and unlock the ship allowing you enough time to go to the Koran planet and do what you need to do but however if it isn't then you could always use it to run away" she said to Twilight.

"Okay what about the crew" Twilight said.

"The crew belong to you they follow you through hell" Celestia said "I am going with Shari to help her now just be ready" they both went away.

…

On the ship Twilight was with the pilot as they had the location that SAFAP had given them to see where he come from now as the light blinked still saying lock down just then the whole board then lighten up with the thing saying unlock "Get us out of here" Twilight said.

"Got it" the pilot said as the ship started to move away from the citadel.

…

after passing through several parts of the galaxy they were starting to get worried "Um are we lost SAFAP" Rainbow Dash said looking out the window seeing nothing.

"No I am at the correct location they are here" he said to her.

"Um James I am detecting hackings going on in the ship" Serena said popping up on board.

"What but that can't be right" James said just then this smoke filled the whole ship "knock out gas" he shouted just as he was knocked out as the others and the whole ship was knocked out.

…

Twilight slowly open her eyes seeing her friends where next to her James, Athena and Rusher as well as the crew of the ship they were all tide up just as every one was coming around "Where are we" Applejack said.

Just then they saw SAFAP in front of them "SAFAP" where are we" Twilight said to him.

"We have arrived" he said to them as they saw these round tall metal robots with what looked like two machine guns at each side as they had four red dots.

"Hay let us go before I knock out into bits" Rainbow Dash shouted to one of them.

Just then one of them turned and walked towards her "I think you made it made" Fluttershy said to her as the robotic thing lifted one of it arms in the air just about to struck but then this three finger hand stopped it as they saw it was that same creator from the CCTV shaking it head as the robot lowered it arm.

But then that creator pointed to three of those robots one two more of those SAFAP to Twilight as they picked her up "Hay let her go" James shouted out to them as they ignored him and walked off into a a lift as they could tell.

…

As Twilight couldn't use her magic as there was something blocking it just then the door open to what looked like a bed room as she saw one of those creator standing at a window as the creator waved it hand as they left "Please let us go we are on a mission an important one" Twilight said as the creator still stood there "Please the galaxy is in danger let us go who are you" she said looking around the room seeing a torn flag of the badge of the Locust Empire "Look okay if you let me go I do what ever you want with me please just let us go and do our job" as she was getting angry "I demand you let us go I am princess Twilight Sparkle" she shouted to the creator.

Just then the creator turned holding a glass as the creator placed the glass on the table and walked over to Twilight as it remover it helmet showing it had four eyes and a tong like a lizard with sharp razor teeth's as she then felt it armoured up hands touching her "Please let us go we have nothing of use to you" she said sounding more scared.

As the creator then stopped in front of her "If I wanted to rape you I would have done that but I am not that kind of thing we both have something in common and you do have something of use to me" the creator said untying her.

"What do you mean" she said scared still.

"Simple you have most of the information on your computers info which belong to us and I saw you when you interact with that beacon" he said almost as if he watched her.

"Who are you" she said to him.

"Simple I am one of the three last Locust from the Locust Empire" he said to her.

"What no but they were wiped out" Twilight said to him shock.

"Lies we put down you see me and the other two had gone into hidden with only two ships because you and I know that the Harvesters will return they did it to my time line just as we were on the verge of unlocking the secretes of those FTL Space Port then they showed up wiping us out of taking us and changing up into those mindless thing" he said sitting down.

"So the FTL Space Port the Citadel isn't your technology" she said taking a seat in front of him.

"No they belong to the others race before us but either way we left message behind in hope the next generation would start preparing for it like your kind we help your kind to a point we felt sorry for you all because you could only count up to four as you only had four hoof then we left you alone like the humans and so on then we wiped all knowledge of you and the others so that the harvesters wouldn't attack you all but us three were placed in a sleep mode so that if any of you failed we would pick up the pieces and carry it on" he said to her.

"Okay say I believe you what proof do you have" she said to him.

"Simple I admire you motivation to life making friends with lots of different things I find you lacking at the will of commanding but I find you interesting a lesser mind would have been killed by what you saw but yet here you stand still alive and strong almost a legend in my book look I can get your ship and all of your friends to Koran my home planet and I will help fight the Harvesters but I will remain out of your council eyes" he said sound strict on that last part.

"Thank you we need to get going then" Twilight said to him.

"Don't worry he won't get far yet" as they both went back into the lift and down.

…

When they arrived Twilight saw her friends and crew all not tide up any more "Don't worry they filled us in so we working together" Applejack said to Twilight.

"Okay so what the plan" Rainbow Dash said to them.

"Well I will lead your ship to the location after that I and four of the heavy guns will come along to fight" the Locust said to them.

"Okay sound like a plan what your name" James said to him.

"Oh my name is Grief that one there" he pointed to a inch smaller Locust "Her name is Crystal and that one there" he pointed to the same size as him "Is Krakow and you can take SAFAP with you he will help you track our ship" he said to them.

"Okay let head back to our ship and we follow them" as they were lead the way they were also taking SAFAP with them.

…

When they were back in their ship they looked out the window and saw two weird looking ships they were much more longer than any ships in the galaxy and they looked more advance than anything they have ever saw except for that Harvester as they began moving they then saw an electric lighting going around both of the ships but what stunned them was they turned invincible "So they have cloaking on their ship to blend in with the background" Athena said amazed by that.

"Yes it is how we moved without being seen but even the harvesters knows where we are" SAFAP said then facing Applejack "Commander Applejack I have chosen" he said.

"Chosen what" Applejack said confused on what he meant.

"A name I have chosen a single name for myself I have chosen COM" he said to her.

"Why" Applejack said to him.

"I could tell you but we would be losing more time now and I suggest we start moving" he said to her.

"Yes let follow them though and stop Thomas once and for all" Twilight said to the pilot as they all got ready.


	6. Chapter 6

**Chapter 6**

When they arrived Twilight had got on the shuttle with Pinkie Pie, Rainbow Dash and James as well as COM was coming as they closed the door and they felt the shuttle moving "Okay we all know what at stake stop Thomas from doing what ever he is up to".

"Commander Twilight I have set up a radio link to the L,E Faith and to Grief" COM said to them all.

"Grief what are you doing" Twilight said to him.

"I am not going to be there fighting the now I am sending Crystal down with five heavy guns and four SAFAP along with two Self Aware Gunships Air Planes or SAGAP for short but I will meet you all on the final run good hunting" he said out as they girls all got them self ready along with James.

…

When they touched the ground Twilight saw a transport plane landing as it cloak came off she was amazed how well their advance is as she then saw those robots coming out with Crystal as they saw her looking around just then they saw two huge planes almost like a fighter plane but with more guns than normal it had lots of missiles and had four machine guns on it two on each side.

"Look like your enemy was here he gone inside that road tunnel but he seem to damage the control we will need to override it from the security office" Crystal said looking at the big huge doors blocking their way to Thomas.

"Okay where that" Rainbow Dash said to her.

"Just across that court yard there is a lift it should take you directly to the office" Crystal said pointing the way just then lot of mindless humans came running out of nowhere "Ah challenge at last let hunt" she said as the five heavy guns and Gunships along with the SAFAP all started to open fire.

"Twilight we make a path you run for the lift and get that door open as secure a transport for us" Crystal shouted out to her as she nodded.

Rainbow Dash saw on of the heavy guns tucked it self into a round ball and started to roll towards the enemy knocking them over making a clear path to the lift "Wow that is so cool" she said as they started to rush for the lift.

Just as they got in the door close and they felt the lift moving up "Okay everyone here" Twilight said as she saw Rainbow Dash, Pinkie Pie and James was all there "Wait where COM" Twilight said worried.

"Commander Twilight do not worry I have a rout to the office the Locust has always made rout for us to get to places I have arrived and will set everything up for your arrival" COM said over the radio.

"Okay" Twilight said as they put their guns down.

…

When the door open they saw COM was just finishing off "Twilight the consul is ready for you just push this button and the door will open" COM said as they saw the green colour consul with a big round button on it.

As Twilight pushed the button as they heard screeching noise as the doors were slowly opening "Crystal we got the doors open" Twilight said over the radio.

"Yes I see we also got ourselves a tank as a transport come back down Thomas has already got enough time ahead of us" she shouted back over the radio.

As they made their way to the lift non of them had no idea what was about to happen at the Citadel.

…

Citadel location

the Galaxy fleet was all ready just as all these ships came out of FTL a long with that huge Harvester "All ships engage the enemy do not let anything through" a human ship captain shouted out over the radio as they started to fire into each other.

"Shadow Might has the Galaxy council on board I repeat we have the galaxy council on board" the captain Arose said over the radio on the ship.

…

Twilight and the others meet back to the door as they saw the tank it had two huge turret head one at the bottom had two long tubes and the one at the top had one long tube as well as a turret gun at the very top "Oh can I get the gun at the top" Pinkie Pie shouted with excitement in her.

"Yes you can" Rainbow Dash said as she cheered out as they all climbed in "wait what about all of them" she looked around the heavy guns.

"Don't worry I radio for a pick up now let get going the gunships have gone ahead to clear us a path so it should be easy where Thomas is going" she said as they all climbed on and the tank moved forwards.

"So who tanks is this" James said to Crystal.

"Oh it mine I call it my pets project which I am naming it triple guns as it got three main guns" Crystal said as they travel through the tunnels seeing the dead bodies of the enemy "See told you it be easy the gunships knows what their doing" she said.

…

After a few hours they were stopped by some force field "Mm could be a trap" James said as they all jumped out of the tank and a door open to a long catwalk "I guess we walk this way the now.

When they came to the end they saw a rad hologram "What this" Pinkie Pie said.

"It one of our main AI build to look after the building "AI what happen" Crystal said to the thing.

"general Crystal welcome to outpost Hammerlocks" the AI said to her.

"I heard about this in myths though what is this place for" she said to it.

"This building is a vital research building the scientist who worked here were on the verge of unlocking the FTL Space Port and had completed a fully working constructed one which link to the main hub in the Citadel" the AI said to her.

"Wait so these pods are full of your kind did they finish what they were building and what this main hub I never heard or saw this thing" James said looking around the room.

"Yes they did and the hub is to unlock an FTL Space Port not like the others this one connected to the Dark Space where it is believed that the Harvesters sleeps there and waits until all life has got to a point in advance the the main hub is connected and unlocking the FTL Space Port to allow the Harvesters through to begin wiping out all life we tried to stop it but sadly their effort has failed them" the AI said to him.

"Okay has an enemy called Thomas made it to the location" Rainbow Dash shouted to it.

"he is getting closer I might suggest you hurry but take this date and place it inside the main hub it will shut down this FTL Space Port stopping the Harvesters return not permanently but it might give you enough time to get ready" the AI said then shutting it self off.

"Okay grab the date and let get going" Twilight said as Rainbow Dash grabbed the date and rushed off with the others back to the tank.

"Grief Thomas is nearing" she was cut off by him.

"I know I am right behind him the now" he said back over the radio.

…

When they came over to a huge open field they saw a small size of a FTL Space Port as they drove the tank at high speed and jumped through the air and was sucked in to the FTL Space Port.

…

When they came crashing into the Citadel lobby as they all climbed out coughing to get air "Well I say that was a great ride can we ride it again" Pinkie Pie said.

"No" they all shouted out the same time.

"My tank" Crystal said looking at her damaged tank "I will make them pay for this" she said patting her tank on the side.

When they looked around they saw the whole place was a war zone fires, dead bodies and so one "This is admiral Shinning Armour any one come in" they head a voice calling over the radio.

"Brother it me" Twilight quickly shouted over the radio.

"Twilight good to hear listen the arms of the Citadel is closed and this huge ship is inside we can't get in the council is on the Shadow Might only Shari and Princess Celestia isn't counted for".

"Got it I get those arms open for you" Twilight said as they rushed into a lift just before the door shut they saw Grief jumping in.

"Ah I ain't out of the game yet" he shouted getting up as they all hugged him.

"Okay so we just have to place the date in the main hub and it should do what that AI said" Rainbow Dash said as the lift was moving to the council chambers.

"Yes as far as we know" Crystal said just as the door open and they all rushed out into the chamber and saw Thomas on this consul.

As they surrounded him as he turned "Ah James I thought you would be dead" he said to him.

"Yer well sorry to say I am not" he said holding his pistol to his head.

"Why Thomas your a Spec Ops you sworn to protect the galaxy" Twilight said to him.

"Twilight you saw what the harvesters can do look at the Locust Empire they tried to fight them but failed but I thought what if they didn't then they would still be here so I am just making a peace between us and them" he said to her.

"You sound wrong he has taken over your mind you body listen to yourself" Twilight said to him.

"He is not I am still in control of myself" she said to her.

"No you not" she said to him.

"So what are you going to arrest me or are you going to kill me" he said smiling to her.

"No I won't arrest you but I can't kill you" she said facing away from him.

"But I can" James said then pulling the trigger as the bullet got him in the head "That for me and Athena home world" he said.

Just then heard the captain on the Shadow Might ship asking for help "This is Shadow Might we are taking heavy damage we can't last any longer in this fight we have the council on board" they heard the captain saying.

"Princess Twilight this Canterlot Defender we are nearing you location with a lot of back up we can go in now and save the Shadow Might but we might lose the fire power to take that thing down" the pilot said to Twilight.

"Grief what about your ships" Twilight said to him.

"My ships are hear but I have told them to cut their communication with that ship they are told to stand by to shoot the harvester down" he said to her.

"Twilight it times like this I think on what more important a few bunch of lifes or an entire galaxy I have always chosen the galaxy" James said to her.

"I am sorry council Canterlot Defender stand by for the arms to open shoot down the harvester" Twilight said with guilt and sadness in her allowing the council to be killed.

…

As Canterlot Defender came out of FTL along with a lot more ships on the Pony ship an admiral spoken on the radio to their ships and the few human ship "Listen up everyone we are going to attack that thing once the arms are open nothing else matters got I repeat nothing else matters" the admiral said over the radio

on Shadow Might the captain Arose pilot shouted to her "Captain there reinforcement it the ponies and human fleet" the pilot said with hope in her.

"Reinforcement this is Shadow Might we need immediate assistant we have" as she was cut off by her pilot.

"Captain they close their radios on us" the pilot said with sadness in her.

"May the goddess forgive us" the captain said as she saw the enemy ship opening fire on her.

As they all saw the Shadow Might getting blown up by the enemy ships just as Twilight pushed the button and placed the date in and the arms opened up as they saw the reinforcement made their move in as well as they saw the two Locust ships hitting the Harvester.

When they saw it explode they saw part of it was heading towards them "RUN!" shouted Twilight as they ran for the door but it was too late.

…

Hours later James, Rainbow Dash and Pinkie Pie was found under the rumble alive as they saw Shari and Celestia helping them out "It okay your safe now" Celestia said helping James out "Where is Twilight" Celestia said as James looked behind him to the part of a huge leg with sadness as Celestia had a tear coming down her.

Just as they were about to walk off they heard running as they looked back and saw it was Twilight alive with a few cuts and scratch but alive as she rushed to Celestia as they both gave each other a hug "It good to see you" Celestia said.

"And same to you" Twilight said as they both let go as James came up to her as he smiled to her and gave her a hand shack "Wait where are the other two" Twilight said as James, Pinkie Pie and Rainbow Dash looked around until Pinkie Pie shouted out.

"There" she pointed to the window as they saw Crystal and Grief waving to them as one of their own transport came up to them uncloak as well as they both walked on to it and even COM was going back with them two as then saw the plane moving away as it cloak came back on.

"Come on let get you all cheeked out" Shari said as they all walked off to the medical.

Four Weeks later

Twilight was called to see Shari and Celestia as she arrived "Princess can I first say I am sorry for not saving the council".

"Twilight it is okay they knew the risk themselves even a Spec Ops should be ready to sacrifice the council to save more lives" as Shari said to her "Now we called you here to see if you want to help us out by joining the council" Shari said to her.

As she gasp with shock in her until she got over quickly "Um it a good offer but I am sorry to say I am turning it down I like to work with my friends more" she said as they both nodded as she walked off but yet there was no mention of the three last Locust as only Twilight her friends James, Athena and Rusher knows about their existing as she heard Shari and Celestia talking about getting ready for Harvester return.


	7. Chapter 7

**Chapter 7**

Four months have passed after the attack on the Citadel and Twilight and her team along with Rusher, James and Athena was patrolling as there was reports of several ships going missing "There nothing on the scanner" Applejack said looking at the computer.

"Well something must have happen several ships gone missing" Rainbow Dash said to her.

"I say it pirates this whole area is crawling with them" she said to her just then a red light came on.

"In coming ship heading on a collision course with us" Serena said to them all.

"Unknown ship every one brace for basic combat" the pilot voice rang out over the speakers on the ship as the alarms went off just then the ship exploded "We are hit" the pilot shouted out.

"Every one get to the escape pods now" Twilight shouted as there was another explosion.

"The pilot won't leave" Rarity shouted to her as they all were rushing around.

"You get to the escape pod I get the pilot out of here now go that an order" Twilight said grabbing her helmet as Rarity nodded and rushed off to the escape pod.

As she went to the main room next to the pilot room she saw a huge gaping hole in the roof and saw the ship it was made out of rocks and metal with what looked like a huge gun at the front as she rushed to the pilot "Come on we need to evacuate" she said to him.

"No I won't leave the ship I can save her" he said to her.

"Don't throw your life away the ship is lost" she said to the pilot as he sigh and got up as she helped him in a near by escape pod just then an explosion had thrown Twilight away from the escape pod as the pilot screamed to her as she couldn't get to the pod as the enemy ship firing in their way as she pushed a button as the escape pod door close and went off just before Twilight thrown away from the ship from an explosion as she banged the back of her head knocking her out and her oxygen tank was cracked open leaking air out as she was was trying to stop the leak but she couldn't the last thing she saw was the ship exploding into bits and the enemy ship moving away.

…

Two years later

Twilight slowly open her eyes and was blinded by a bright light as she heard bleeping noise and two voice a female voice and a male voice "She coming around" the male voice said.

"She is not ready to wake up quick give her the sensitive to knock her out Commander Twilight please stay still the female voice said as Twilight was breathing heavy just then she was knocked out again just catching the last few words.

"I told you those reading were wrong" the female voice was the only thing she heard.

…

"Commander Twilight wake up" Twilight heard that female voice as she slowly woken up just as the room rumbled with explosion "Twilight wake up we are under attack grab that pistol" the voice said.

As Twilight woken up and saw the pistol as she looked at it "Wait this gun doesn't have a clip" she said.

"It a medic room what do you expect we will get you a clip through that door now move the security bots are killing everyone" the voice said to her.

As she moved as the door open and saw four clips on the ground as she picked them up and loaded the gun and walked on down a corridor just then she saw two security bots walking in as she shot them two in the head as they fell to the ground.

"Twilight you have to... hold on" Twilight heard an explosion "Twilight get to the evacuation area I am under attack" the voice said before it was gone.

As she walked on she open a door to a small room looking like a office she saw a log as she pushed it and it played "We got Twilight form the sight Ravel has assured me that she is salvageable she has suffered a lot of from being hit at the back of the head and as well lose of air but the project will go ahead" then the log ended.

"Wow I must have been in some mess" Twilight said to herself as she then walked on.

She came to a room where there was two walkways next to each other on one side was lot of those security bots and on the other was a unicorn pony stallion wearing a helmet and a uniform not like the Equestrian uniform holding a pistol shooting those security bots down as she quickly got to him "What going on here" Twilight said to him.

"I thought you were still knocked out well guess thing are bad if Trixie got you running around look I tell you once we have dealt with these" he said shooting one in the head.

"Got it" as Twilight shot another one in the head as they both then got up shooting the security bots down.

When it was over Twilight looked at him "Who are you" she said.

"I am Rena I am a gun hire I" he said reloading his gun.

"Where am I and what happen to me and my friends" she asked him.

"Your one a medical ship and your ship was attack and you were put down as Killed in Action but we found you and brought you back your friends we have no idea" he said to her.

"Is any one still alive on this channel" a male voice called out over the radio.

"Ravel is that you where are you" Rena said over the radio.

"I am over at wing D please can you get to me the security bots are coming after me" he said sounding scared.

"Okay we are coming let get going" he said facing Twilight.

"Okay let go you lead the way" Twilight said as he nodded and they both went off through the door as they rushed down the corridor and up the stairs as they shot down two security bots in the head and got into the lift as they felt it going up.

…

When the door open they saw a earth pony stallion pony in a white coat injured as they shot the only one security bot there "Ravel are you okay um Twilight there should be a medic gel on that table" as Rena pointed to the table as Twilight got it it was a red box with a white cross as she gave him the medic gel and saw him opening it up as there was all sort of things in there as he placed this gel on and it healed the wound up quickly.

"Thanks" he said getting up.

"Wait your voice you where there when I came around" Twilight said to him.

"Yer that was me I thought I could shut the security bots down from here but can't come we need to get out of here the shuttle bay" he said to them both.

"Wait about Trixie" Rena said to him.

"Look we all knew the rules if she isn't here then she is dead" he said to him.

"Wait Trixie just helped me" Twilight said to him.

"Well maybe not dead but still let go now" he said opening the door just then Trixie was on the other side holding a gun to him "Trixie you were" he never finished off saying as he was shot dead.

"Dead yes well sorry come quick" she said to them both.

"Wait you just shot him why" Twilight said her.

"Twilight Sparkle I remember you before you became a princess look he betrayed us all he hacked the security bots to attack us all he killed all of my team" she said to her.

As she sigh "Okay I don't trust any of you yet but let get off this station" Twilight said as they all walked off to the shuttle.

…

"So how long was I out for" Twilight asked them.

"You were out for 2 years and four months and 20 days" Rena said to her as she gasp in shock in her.

"We are heading to another base look we work for a corporation called Cobra that boss want to see you there" Trixie said to her.

"Wait I heard of you, your all a bunch of murders I will not work for you" she said angry about the this.

"Look hear what the boss has to say first" Rena said as they all got comfortable on the shuttle.

…

When they arrived at a base Twilight was lead to a room where this orange light was scanning her and then the room filled with darkness and a cloaked pony size was in front of her "commander Twilight" the pony said in a male voice.

"The boss I take it" she said to him as he nodded "So what you need me for".

"Simple while you were out colonies have gone missing ponies colonies there are no evidence to what happen the council is doing nothing about it and I want to do something about it but I needed you" he said smoking.

"Okay say I believe you what proof do you have" Twilight said to him.

"Simple go to project Harmony and see the evidence your self if you don't find it then you can go your own way take Trixie and Rena with you" the boss said to her.

As Twilight sigh and walk away to meet Trixie and Rena as she saw them both at separate ends of the room "okay so what this project Harmony" she ask Rena.

"Well it a friendship project for all race of the galaxy can come here and live under the one place in peace" Rena said to her.

"Right the shuttle is ready let go" Trixie said to both of them as they all walked to the shuttle bay to get going.


	8. Chapter 8

**Chapter 8**

When they arrived and jumped off the shuttle they saw the place deserted not a single soul around "What happen here" Twilight said looking around the place.

"Don't know there is no signs of gunshots or anything" Rena said as they walked up to a building and the door slide open as they saw cups and other thing all over the place "Looks like they got up and left in a hurry" Rena said as they walked through the building.

Just then they heard a noise as they pulled out their guns as it was coming from another room of the building as Trixie pushed a button and the door open just then they were meet with three Arose commandos elite holding their guns to them just then another one jumped in the middle of them.

"Nolan stop I am in charge" as the one in command turned and gasp "Twilight is that you" she said with a shock look on her.

Twilight looked careful and then gasp "Rusher is that you".

"Yes it me I thought you were dead" she said looking at her then to the other.

"Forgive me for not letting my gun down to you Cobra scum" said one of the Arose to them.

"Nolan calm down" Rusher said to her.

"What are you doing here" Twilight asked her.

"One of our kind came here to help out the project but we didn't heard from her so we came here to cheek out" she was then cut off by the one of the commandos called Nolan.

"Yer but we saw her she wasn't her self when she saw us landing she ran to a warehouse" she was then stopped by Rusher.

"It true we don't what happen to her but she seemed different and she had activated the security bots to attack any one" Rusher said to her.

"Okay let team up together but you and your teams cane go around the far side while I and them two take the direct route" Twilight said to her.

"What we working with Cobra" Nolan said to Rusher.

"No your working for me remember if you don't like it then you can get your ass back on the ship" Rusher said as Nolan sigh in defeat.

…

As they both spilt up and carried on they open a door and saw four security bots landing in front of them as they pulled out their weapons and ducked in cover shooting them in the head or any where they can.

After they killed the last on they carried on by climbing down a ladder to the ground "Twilight Nolan and her team went ahead to get her first they want to stop you" Rusher said over the radio.

"Got it" Twilight said as they worked through building and other structures that were abandoned.

…

They came to a huge door "Twilight we have a problem there is a heavy security mech that blocking the door to the warehouse listen I am opening the door in front of you" Rusher said over the radio.

"Okay you two get in cover and be ready" Twilight said to Trixie and Rena as they all got behind walls.

Just then the doors began to open as Twilight looked and saw the arose commandos being killed by a huge robot security as it had a rocket launcher and a gun as they moved behind walls Twilight saw a small personal rocket launcher as she jumped to grab it while the others kept the thing busy she aimed at the robot and shot one rocket as it flew through the air and hits the robot exploding it into bits.

Twilight got up and saw Rusher was attending to the commandos who were injured in that fight "Rusher" Twilight said to her.

"Don't worry you go on ahead to get Coleraine to that door to the warehouse I stay here and look after the wounded" Rusher said Twilight helping to heal a commandos leg.

Twilight and her team got to the door and open it and saw her sitting in front of lot of screen she was talking to herself "Must hide monsters will come back to get me".

"Coleraine" Twilight to her while walking up to her.

"No no Coleraine here must stay quiet" she said looking over all the screens.

"We need to grab her attention" Trixie said to Twilight.

As Twilight brought up her hoof and pushed a few buttons on her tool as it something to the screens as Coleraine stopped and look behind her and saw them "Your still here the monsters never saw you" she said looking around them.

"Calm down we need to know what happen" Twilight said in a calm voice.

"You mean you never saw well I saw everything here look" she pushed a button and the screen shown these creators on four legs pushing these weird thing and there was lots of what looked like tiny bugs "The monster taken everyone and left" she said I had gathered the date on my tool".

"We need that date well need to take her with us" Rena said to Twilight.

"What no Coleraine need medic treatment" Rusher said behind them all.

"But we need the info" Rena said to her.

"Twilight please" Rusher said to Twilight.

"Coleraine needs help so she will go with Rusher I am sure we can transfer the date into my tool" Twilight said they agreed on that and Coleraine had given her the info as Rusher help her out she stopped and looked to Twilight one more time "Thank you Twilight I am glad your still in charge" she said then walking away.

"Come on let get back" Trixie said as they walked back to the shuttle.

…

When they got back to the base Twilight was with the boss "Did we find out who was doing this" Twilight asked.

"Yes it turns out to be a race known as the Menarche" the boss said to her putting the fag out.

"What but don't they keep to themselves and what do we know about them" Twilight said shocked by this info.

"Very little they are well advance they only come out of the Travers area to gather some thing and then go back into there" he said pulling out another fag and lighting it.

"What the Travers about" Twilight said to him.

"It a system where no ships have came back through it but if they go through it then they must have the harvester techs on their ships" he said thinking to himself.

"Then we need to hit them first" Twilight said him.

"Yes I have a list here of names they have some info on those race and I have some names to team" he was cut off by Twilight.

"Keep those names for teams I had a team Where is Rainbow Dash" Twilight said to him as she hoped her friends would help her.

"That was two years ago thing have changed Rainbow Dash has been promoted to admiral along with your Brother" he said taking a puff of his fag.

"Where Applejack" Twilight said to him.

"Applejack had left the military and gone back to her farm to help out now" he said taking another puff of his fag.

"Where Pinkie Pie" Twilight said.

"Pinkie Pie had gone back to the café shop to help out Mrs and miss cake" he said to her through the smoke of his fag.

"What about Rarity" Twilight asked.

"Rarity also gone back to her shop she is carrying on her fashion work making dress and that" he said putting out his fag.

"Fluttershy what about her" she said to him.

"Fluttershy also left the army to open up her own vet for animals which is going great" he said then got up to move about.

"What about captain Athena and James" she said wondering about them two.

"Captain Athena and James had gone off grid I don't know where they are at the moment" he said turning to face her.

"Okay what about the Galaxy council I am still Spec Ops" Twilight to him thinking about that idea.

"They have said they were going to do something about it but they never did if you can get them to help then all by means do so and Twilight I have a ship for you I think you will like it and I have track a pilot I heard he is one of the best I will still send those list of names to you" he said and then he went off line.

"Hay princess Twilight" Twilight heard that same voice as she turned to see it was the pilot who had flew the Canterlot Defender.

"Hay what been going on" she said happy to see a face she knew as they both walked out of that room.

"Well after the ship blew up and you went missing we couldn't find your body so they council said you were killed and reassigned us all but most of us gone our own way" he said as they turned corners "And hay I look at it this way I get to fly again and with this" he said pointing to the window as the light had gone on showing a huge room big enough to fit a ship in as they both gasp at seeing the same style as the Canterlot Defender.

"She will need a name" Twilight said as they both smile as they had a name already "Come on let get going first stop Citadel" Twilight said as they both gone on to the ship.


	9. Chapter 9

**Chapter 9**

When the ship came to the Citadel it had it name painted on the side of it Canterlot Defender 2 as they had docked and Twilight went to the embassy to see someone there.

She came to a office and open the door as Celestia looked and gasp "Twilight your alive so the reports are true" she said sounding happy and rushed up to her giving her a hug.

"Yes I am alive thank you so what happen when I was gone" Twilight said as they both sat down.

"Well big things have changed new ambassadors has taken on the council but I ma guessing your not here for that" she said with a smirk on her.

"Yes I am here to say I need the council help I am going after the race called Menarche" she said to her.

"I see look there not much I can really do here all I can do is keep the council out of your way the now but I will need to tell them that one of their Spec Ops is alive and back in action oh here" Celestia pulled out a laptop and Twilight saw it was her Spec Ops on.

"My laptop" she said smiling.

Just then the door open to Shari coming in as she gasp "Commander Twilight your alive I was so upset hearing the ship was destroyed and you reported dead" she said sounding happy.

"Yes I heard how are things with you" she said to her.

"Oh the same old things" she said to her.

"Well I need to get going I speak to you later" Twilight got up and left the room and heading back to the ship.

…

On board she came to the pilot "Set a course for home Equestria" she said as the pilot saluted and moved the ship out of the docking bay.

"Commander Twilight I have set up the list for you who is more important and who is lest important" Trixie said to her.

"Thank you" she said "Anything else" Twilight said.

"Hello Commander Twilight" a unknown voice called out as a blue hologram came up on a board it was a round ball.

"An AI" Twilight said to the thing while looking it over.

"Actually I am not just an AI I am the ships Artificial cyber Advance Warfare or ACAW I deal with the stocks handling the ships powers, oxygen and other task and in battle I can hack into ships computer and stop them from hacking into the ship" the hologram female voice said to Twilight.

"Wow that is imprests" Twilight said walking off to explore the ship more.

…

When they arrived Twilight saw Ponyville it had grown in size now more population had came to the town but most of the old stuff is still there she saw Applejack farm still out in the edge of town as the ships door open to the huge ships docking bay as there was lot of other ships from cargo carries to normal passengers ships.

As she walked off towards Applejack fist but she bumped into a pink flash "Pinkie Pie" she said.

As Pinkie Pie stopped and gasp in mid air and then screamed out with joy in her "Twilight you alive yeah I have to throw you a super party" she said to her.

"Um not right now Pinkie Pie I am on a mission and I was wondering if you like to come now going on this one means we might not make it back" Twilight said calming the pony down a little.

"Of course I will I don't want to leave a friend behind" she said to her.

"Thank you meet you back here on this ship oh and um we working with Cobra the now" she said rushing off to Applejack farm.

…

When she arrived she saw Applebloom working with Applejack on bucking trees as she got close "Why not use magic" Twilight said.

Applejack stopped and turned slowly and gasp with tears coming down her "Twilight is it really you" she said feeling her.

"Yes it is" she said smiling as they both hugged into each other.

"It good to see your fine and alive I was so worried when you staid behind on the ship" she said to Twilight.

"Yes same here listen I am going on a mission" Twilight said to her as they both sat down "And it one where I might not come back from and I would like you to come on this mission but it working with Cobra" Twilight said hoping she would come.

"Twilight Cobra that a murderous company" she faced Twilight.

"I know but they are wanting to help those colonies who went missing" Twilight said to her

"Okay Twilight I help you" she sigh in defeat and got up as they hugged into each other "Right I gather my things and meet you at the ship docking bay" Applejack then went off while Twilight went off to meet Rarity.

…

When she arrived at Rarity shop she saw Rarity doing up a dress "Welcome please take a seat I will be with you in a moment" Rarity saw not even looking towards the door.

"Hello Rarity" Twilight saw her dropping the pins and cloths as she turned with a shock and tears as they both rushed to each other giving a hug.

"Twilight your alive" Rarity said through her tears.

"Yes I am and I am here to see if you will join me on a mission one where you might not come back" she said as Rarity sigh.

"Twilight I left the army now I moved on" Rarity said looking out the window.

"I know but we need you it the colonies they need us the elements of harmony" Twilight said to her.

"Okay I will come with you"Rarity said worried on where this might go.

"Thank you meet the others down at the shipping docks now I need to get Fluttershy" Twilight rushed off.

…

When Twilight found Fluttershy at her cottage as nothing had changed from it still the same as it always been she knocked on the door and Fluttershy open it but she gasp "Twilight your alive".

"Yes Fluttershy I am can I come in" Twilight ask as Fluttershy opened the door and let her in as she walked in seeing Angle Bunny hopping around "Fluttershy I need your help on a mission one where it involve fighting Menarche to save hundred of Colonies" Twilight said.

"Oh I don't know" Fluttershy said unsure of what to do.

"Please Fluttershy we need you" Twilight plead with her.

"Okay I come" Fluttershy said as Twilight smiled in happy.

"Thank you come let meet the others at the docks" Twilight and Fluttershy went walking towards the dock "Oh don't worry I get Spike to look after the animals for you like last time" Fluttershy smiled at that idea and knowing that her animals will be look after.

…

When they two arrived they saw every one there talking about the new Canterlot Defender as Twilight was in front of them "Okay here is the truth we will be working with the company called Cobra and we are going after a race called Menarche they are the ones behind the missing colonies and I am going after them to stop them once I get Rainbow Dash on our side but I won't lie here we might not make it back we know how advance they are but I ain't letting them get away with this so I am going to show them what happens when they mess with us ponies we will show them what we are made off now you can come with me or not I won't hate you for the choice you make" Twilight said to them making sure they are still on this mission.

As they all nodded "We are coming Twilight" Applejack said as they all got on board.

"Okay Rainbow Dash is at the ship yard of Azores waiting for a new ship to take command of it so there the best place to get her" Applejack said to Twilight as they both made their way to the ship.

…

When they got on the ship every one was shock to see Trixie was working for Cobra but they soon let that go by and they saw they had their old pilot "Okay pilot take us to the Ship Yard of Azores quickly" Twilight said as the pilot nodded as they felt the ship moving.

…

After they all were shown around the ship they heard the ship pilot talking "Commander Twilight we have arrived at the ship yard" he said.

"Got it let go get Rainbow Dash back" she said walking to the ships door.

When the door open she walked out and saw the huge yard full of ships some nearly complete others just started to be worked on as she walked on she saw a huge building with the sign sawing Yards HQ where there was humans and other race coming in and out of.

When she entered she saw the place was busy until she heard Rainbow Dash voice behind her "Rainbow Dash" she turned to see her arguing with a pony behind a desk.

"Twilight your alive" she said shock and happy.

As they both rushed to each other hugging into each other "Yes I am".

"So what are you here for" she said letting her go as they both sat down on a near by bench.

"Well I am here for you I need to ask you if you would come on a mission with me to take down the Menarche but it will be working with Cobra" she said to her.

"Okay I come" was all she said.

"What just like that" Twilight was stunned on that.

"Yer trust me Twilight I am sick off this place I have been here for four days waiting for my new ship destroyer which they said it should have been ready four days ago so I wouldn't mind to get away from all this" Rainbow Dash said to her.

"Okay then let go then" she then taken a radio "Pilot get ready we are now going to the Omega to get the info" Twilight said as they both walked back to the ship.


End file.
